Indexing the positions of continuously moving objects
SIGMOD '00 Proceedings of the 2000 ACM SIGMOD international conference on Management of data
Management of Dynamic Location Information in DOMINO
EDBT '02 Proceedings of the 8th International Conference on Extending Database Technology: Advances in Database Technology
On the Generation of Spatiotemporal Datasets
SSD '99 Proceedings of the 6th International Symposium on Advances in Spatial Databases
Managing Location Stream Using Moving Object Database
DEXA '03 Proceedings of the 14th International Workshop on Database and Expert Systems Applications
TMO-Structured Distributed Location Information System Prototype
ISORC '05 Proceedings of the Eighth IEEE International Symposium on Object-Oriented Real-Time Distributed Computing
Distributed Scalable Location Data Management System Based on the GALIS Architecture
WORDS '05 Proceedings of the 10th IEEE International Workshop on Object-Oriented Real-Time Dependable Systems
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RNA interference (RNAi) is a posttranscriptional gene silencing mechanism used to study gene functions, inhibit viral activities, and treat diseases therapeutically. However, RNAi has off-target effects--non-target genes can be unintentionally silenced. Therefore, target validation through target detection is crucial for the success of RNAi experiments. Effective target detection must examine each gene expressed by an organism, making computational efficiency a critical issue. We develop efficient sequential and parallel search algorithms using RNA string kernels, which model mismatches, G-U wobbles, bulges, and the seed region in the hybridization between an siRNA and its target mRNA. Empirical results demonstrate that our algorithms achieved speedups of six orders of magnitude over the alignment algorithm based on tests in the organisms of S. pombe, C. elegans, D. melanogaster, and human. Our design strategy also leads to a framework for efficient, flexible, and portable string search algorithms allowing for inexact matches.